Table of Contents - RDoc Documentation

Pages

• README
  • MiGA: Microbial Genomes Atlas
  • For the impatient
  • How to cite MiGA
  • Authors
  • License

Classes/Modules

• File
• MiGA
• MiGA::Cli
• MiGA::Cli::Action
• MiGA::Cli::Action::About
• MiGA::Cli::Action::Add
• MiGA::Cli::Action::AddResult
• MiGA::Cli::Action::Archive
• MiGA::Cli::Action::ClassifyWf
• MiGA::Cli::Action::Cmd
• MiGA::Cli::Action::Console
• MiGA::Cli::Action::Daemon
• MiGA::Cli::Action::Date
• MiGA::Cli::Action::Db
• MiGA::Cli::Action::DerepWf
• MiGA::Cli::Action::Doctor
• MiGA::Cli::Action::Doctor::Base
• MiGA::Cli::Action::Doctor::Databases
• MiGA::Cli::Action::Doctor::Distances
• MiGA::Cli::Action::Doctor::Operations
• MiGA::Cli::Action::Download
• MiGA::Cli::Action::Download::Base
• MiGA::Cli::Action::Download::Gtdb
• MiGA::Cli::Action::Download::Ncbi
• MiGA::Cli::Action::Download::Seqcode
• MiGA::Cli::Action::Edit
• MiGA::Cli::Action::Env
• MiGA::Cli::Action::Files
• MiGA::Cli::Action::Find
• MiGA::Cli::Action::Generic
• MiGA::Cli::Action::Get
• MiGA::Cli::Action::GtdbGet
• MiGA::Cli::Action::IndexWf
• MiGA::Cli::Action::Init
• MiGA::Cli::Action::Init::DaemonHelper
• MiGA::Cli::Action::Init::FilesHelper
• MiGA::Cli::Action::Lair
• MiGA::Cli::Action::Ln
• MiGA::Cli::Action::Ls
• MiGA::Cli::Action::NcbiGet
• MiGA::Cli::Action::New
• MiGA::Cli::Action::NextStep
• MiGA::Cli::Action::Option
• MiGA::Cli::Action::PreprocWf
• MiGA::Cli::Action::QualityWf
• MiGA::Cli::Action::Rm
• MiGA::Cli::Action::Run
• MiGA::Cli::Action::SeqcodeGet
• MiGA::Cli::Action::Stats
• MiGA::Cli::Action::Summary
• MiGA::Cli::Action::TaxDist
• MiGA::Cli::Action::TaxIndex
• MiGA::Cli::Action::TaxSet
• MiGA::Cli::Action::TaxTest
• MiGA::Cli::Action::Touch
• MiGA::Cli::Action::Wf
• MiGA::Cli::Base
• MiGA::Cli::ObjectsHelper
• MiGA::Cli::OptHelper
• MiGA::Common
• MiGA::Common::Format
• MiGA::Common::Hooks
• MiGA::Common::Net
• MiGA::Common::Path
• MiGA::Common::SystemCall
• MiGA::Common::WithDaemon
• MiGA::Common::WithDaemonClass
• MiGA::Common::WithOption
• MiGA::Common::WithResult
• MiGA::Daemon
• MiGA::Daemon::Base
• MiGA::Dataset
• MiGA::Dataset::Base
• MiGA::Dataset::Hooks
• MiGA::Dataset::Result
• MiGA::Dataset::Result::Add
• MiGA::Dataset::Result::Ignore
• MiGA::Dataset::Status
• MiGA::Dataset::Type
• MiGA::Error
• MiGA::Json
• MiGA::Lair
• MiGA::Metadata
• MiGA::MiGA
• MiGA::Parallel
• MiGA::Project
• MiGA::Project::Base
• MiGA::Project::Base::Float
• MiGA::Project::Dataset
• MiGA::Project::Hooks
• MiGA::Project::Result
• MiGA::RemoteDataError
• MiGA::RemoteDataMissingError
• MiGA::Result
• MiGA::Result::Base
• MiGA::Result::Dates
• MiGA::Result::Source
• MiGA::Result::Stats
• MiGA::Result::Versions
• MiGA::SQLite
• MiGA::SystemCallError
• MiGA::TaxDist
• MiGA::TaxIndex
• MiGA::TaxIndexTaxon
• MiGA::Taxonomy
• MiGA::Taxonomy::Base
• Net
• String

Methods

• ::DEBUG — MiGA::MiGA
• ::DEBUG_OFF — MiGA::MiGA
• ::DEBUG_ON — MiGA::MiGA
• ::DEBUG_TRACE_OFF — MiGA::MiGA
• ::DEBUG_TRACE_ON — MiGA::MiGA
• ::DISTANCE_TASKS — MiGA::Project
• ::EXCLUDE_NOMARKER_TASKS — MiGA::Dataset
• ::EXCLUDE_NOREF_TASKS — MiGA::Dataset
• ::EXECS — MiGA::Cli
• ::FILE_REGEXP — MiGA::Cli
• ::INCLADE_TASKS — MiGA::Project
• ::INFO_FIELDS — MiGA::Dataset
• ::INPUT_TYPES — MiGA::Cli::Action::Add
• ::KNOWN_RANKS — MiGA::Taxonomy
• ::KNOWN_TYPES — MiGA::Dataset
• ::KNOWN_TYPES — MiGA::Project
• ::LONG_RANKS — MiGA::Taxonomy
• ::ONLY_MULTI_TASKS — MiGA::Dataset
• ::ONLY_NONMULTI_TASKS — MiGA::Dataset
• ::OPERATIONS — MiGA::Cli::Action::Doctor
• ::OPTIONS — MiGA::Dataset
• ::OPTIONS — MiGA::Project
• ::PREPROCESSING_TASKS — MiGA::Dataset
• ::RESULT_DIRS — MiGA::Project
• ::RESULT_DIRS — MiGA::Result
• ::RESULT_DIRS — MiGA::Dataset
• ::TASK_ALIAS — MiGA::Cli
• ::TASK_DESC — MiGA::Cli
• ::aai_path — MiGA::TaxDist
• ::aai_pvalues — MiGA::TaxDist
• ::aai_taxtest — MiGA::TaxDist
• ::create — MiGA::Result
• ::daemon_home — MiGA::Daemon
• ::debug? — MiGA::MiGA
• ::debug_trace? — MiGA::MiGA
• ::default_opts — MiGA::SQLite
• ::default_opts — MiGA::Json
• ::distribute — MiGA::Parallel
• ::exist? — MiGA::Project
• ::exist? — MiGA::Result
• ::exist? — MiGA::Metadata
• ::exist? — MiGA::Dataset
• ::generate — MiGA::Json
• ::generate_fast — MiGA::Json
• ::generate_plain — MiGA::Json
• ::generic_transfer — File
• ::initialized? — MiGA::MiGA
• ::json_create — MiGA::Taxonomy
• ::load — MiGA::Metadata
• ::load — MiGA::Result
• ::load — MiGA::Cli::Action
• ::load — MiGA::Project
• ::new — MiGA::Result
• ::new — MiGA::SQLite
• ::new — MiGA::Dataset
• ::new — MiGA::Daemon
• ::new — MiGA::Cli::Action
• ::new — MiGA::TaxIndex
• ::new — MiGA::TaxIndexTaxon
• ::new — MiGA::Taxonomy
• ::new — MiGA::Lair
• ::new — MiGA::Metadata
• ::new — MiGA::Project
• ::new — MiGA::Cli
• ::normalize_rank — MiGA::Taxonomy
• ::parse — MiGA::Json
• ::process — MiGA::Parallel
• ::rc_path — MiGA::MiGA
• ::thread_enum — MiGA::Parallel
• #<< — MiGA::TaxIndex
• #<< — MiGA::Taxonomy
• #[] — MiGA::Taxonomy
• #[] — MiGA::Cli
• #[] — MiGA::Result
• #[] — MiGA::Metadata
• #[]= — MiGA::Metadata
• #[]= — MiGA::Cli
• #[]= — MiGA::Result
• #activate! — MiGA::Dataset
• #active? — MiGA::Common::WithDaemon
• #active? — MiGA::Project
• #active? — MiGA::Dataset
• #add_alternative — MiGA::Taxonomy
• #add_child — MiGA::TaxIndexTaxon
• #add_dataset — MiGA::TaxIndexTaxon
• #add_dataset — MiGA::Project::Dataset
• #add_file — MiGA::Result
• #add_files — MiGA::Result
• #add_hook — MiGA::Common::Hooks
• #add_metadata — MiGA::Cli::ObjectsHelper
• #add_result — MiGA::Common::WithResult
• #add_result_assembly — MiGA::Dataset::Result::Add
• #add_result_cds — MiGA::Dataset::Result::Add
• #add_result_distances — MiGA::Dataset::Result::Add
• #add_result_essential_genes — MiGA::Dataset::Result::Add
• #add_result_mytaxa — MiGA::Dataset::Result::Add
• #add_result_mytaxa_scan — MiGA::Dataset::Result::Add
• #add_result_raw_reads — MiGA::Dataset::Result::Add
• #add_result_read_quality — MiGA::Dataset::Result::Add
• #add_result_ssu — MiGA::Dataset::Result::Add
• #add_result_stats — MiGA::Dataset::Result::Add
• #add_result_taxonomy — MiGA::Dataset::Result::Add
• #add_result_trimmed_fasta — MiGA::Dataset::Result::Add
• #add_result_trimmed_reads — MiGA::Dataset::Result::Add
• #add_versions — MiGA::Result::Versions
• #advance — MiGA::Cli
• #advance — MiGA::MiGA
• #alive_file — MiGA::Common::WithDaemon
• #alive_file — MiGA::Common::WithDaemonClass
• #all_datasets — MiGA::TaxIndexTaxon
• #all_options — MiGA::Common::WithOption
• #alternative — MiGA::Taxonomy
• #ask_for_optional — MiGA::Cli::Action::Init
• #ask_user — MiGA::Cli
• #assert_has_option — MiGA::Common::WithOption
• #assert_valid_option_value — MiGA::Common::WithOption
• #banner — MiGA::Cli::OptHelper
• #bypass_maintenance? — MiGA::Daemon::Base
• #call_cli — MiGA::Cli::Action::Wf
• #cannid — MiGA::Cli::Action::TaxDist
• #check_additional_files — MiGA::Cli::Action::Init::FilesHelper
• #check_and_install_library — MiGA::Cli::Action::Init
• #check_bidir — MiGA::Cli::Action::Doctor::Distances
• #check_cds — MiGA::Cli::Action::Doctor::Operations
• #check_configuration_script — MiGA::Cli::Action::Init::FilesHelper
• #check_datasets — MiGA::Daemon
• #check_db — MiGA::Cli::Action::Doctor::Distances
• #check_directories — MiGA::Lair
• #check_dist — MiGA::Cli::Action::Doctor::Distances
• #check_dist_eval — MiGA::Cli::Action::Doctor::Base
• #check_dist_fix — MiGA::Cli::Action::Doctor::Base
• #check_dist_recompute — MiGA::Cli::Action::Doctor::Base
• #check_ess — MiGA::Cli::Action::Doctor::Operations
• #check_files — MiGA::Cli::Action::Doctor::Operations
• #check_libraries — MiGA::Cli::Action::Init
• #check_mdfiles — MiGA::Cli::Action::Doctor::Operations
• #check_mts — MiGA::Cli::Action::Doctor::Operations
• #check_mytaxa_database — MiGA::Cli::Action::Init::FilesHelper
• #check_mytaxa_scores — MiGA::Cli::Action::Init::FilesHelper
• #check_phyla_lite — MiGA::Cli::Action::Init::FilesHelper
• #check_project — MiGA::Daemon
• #check_rdp_classifier — MiGA::Cli::Action::Init::FilesHelper
• #check_refdb — MiGA::Cli::Action::Doctor::Operations
• #check_software_requirements — MiGA::Cli::Action::Init
• #check_sqlite3_database — MiGA::Cli::Action::Doctor::Databases
• #check_start — MiGA::Cli::Action::Doctor::Operations
• #check_status — MiGA::Cli::Action::Doctor::Operations
• #check_tax — MiGA::Cli::Action::Doctor::Operations
• #check_type — MiGA::Dataset::Type
• #clade? — MiGA::Project
• #clean! — MiGA::Result
• #clean? — MiGA::Result
• #clean_fasta_file — MiGA::Common::Format
• #cleanup — MiGA::Cli::Action::Wf
• #cleanup_distances! — MiGA::Dataset::Result
• #cli_base_flags — MiGA::Cli::Action::Download::Base
• #cli_filters — MiGA::Cli::Action::Download::Base
• #cli_name_modifiers — MiGA::Cli::Action::Download::Ncbi
• #cli_name_modifiers — MiGA::Cli::Action::Download::Seqcode
• #cli_name_modifiers — MiGA::Cli::Action::Download::Gtdb
• #cli_save_actions — MiGA::Cli::Action::Download::Base
• #cli_task_flags — MiGA::Cli::Action::Download::Gtdb
• #cli_task_flags — MiGA::Cli::Action::Download::Seqcode
• #cli_task_flags — MiGA::Cli::Action::Download::Ncbi
• #close_rc_file — MiGA::Cli::Action::Init::FilesHelper
• #closest_relatives — MiGA::Dataset
• #complete — MiGA::Cli::Action
• #complete — MiGA::Cli::Action::Generic
• #complete — MiGA::Cli::Action::Db
• #compute_stats — MiGA::Result::Stats
• #configure_bash_daemon — MiGA::Cli::Action::Init::DaemonHelper
• #configure_daemon — MiGA::Cli::Action::Init::DaemonHelper
• #configure_qsub_msub_daemon — MiGA::Cli::Action::Init::DaemonHelper
• #configure_slurm_daemon — MiGA::Cli::Action::Init::DaemonHelper
• #configure_ssh_daemon — MiGA::Cli::Action::Init::DaemonHelper
• #create — MiGA::Metadata
• #create — MiGA::Result
• #create — MiGA::Project
• #create_project — MiGA::Cli::Action::Wf
• #created — MiGA::Metadata
• #daemon — MiGA::Common::WithDaemon
• #daemon — MiGA::Project
• #daemon_first_loop — MiGA::Lair
• #daemon_first_loop — MiGA::Daemon
• #daemon_home — MiGA::Common::WithDaemonClass
• #daemon_home — MiGA::Daemon
• #daemon_loop — MiGA::Daemon
• #daemon_loop — MiGA::Lair
• #daemon_name — MiGA::Daemon
• #daemon_name — MiGA::Lair
• #data — MiGA::Metadata
• #dataset — MiGA::Project::Dataset
• #dataset_names — MiGA::Project::Dataset
• #dataset_names_hash — MiGA::Project::Dataset
• #dataset_names_set — MiGA::Project::Dataset
• #dataset_ref_active — MiGA::Project::Dataset
• #dataset_ref_active! — MiGA::Project::Dataset
• #datasets — MiGA::Project::Dataset
• #datasets_count — MiGA::TaxIndexTaxon
• #declare_alive — MiGA::Common::WithDaemon
• #declare_alive_loop — MiGA::Common::WithDaemon
• #default_hooks — MiGA::Common::Hooks
• #default_hooks — MiGA::Project::Hooks
• #default_hooks — MiGA::Dataset::Hooks
• #default_options — MiGA::Common::WithDaemon
• #default_opts_for_wf — MiGA::Cli::Action::Wf
• #defaults= — MiGA::Cli
• #define_software — MiGA::Cli::Action::Init
• #delete_alternative — MiGA::Taxonomy
• #dir — MiGA::Result
• #discard_excluded — MiGA::Cli::Action::Download::Base
• #domain — MiGA::Taxonomy
• #done_at — MiGA::Result::Dates
• #done_preprocessing? — MiGA::Project::Dataset
• #done_preprocessing? — MiGA::Dataset::Result
• #download_datasets — MiGA::Cli::Action::Wf
• #download_entries — MiGA::Cli::Action::Download::Base
• #download_file_ftp — MiGA::Common::Net
• #dup — MiGA::Taxonomy
• #each — MiGA::Metadata
• #each_daemon — MiGA::Lair
• #each_database_file — MiGA::Cli::Action::Doctor::Databases
• #each_dataset — MiGA::Project::Dataset
• #each_dataset_profile_advance — MiGA::Project::Dataset
• #each_file — MiGA::Result
• #each_project — MiGA::Lair
• #each_result — MiGA::Common::WithResult
• #empty_action — MiGA::Cli::Action::Init
• #empty_action — MiGA::Cli::Action::Db
• #empty_action — MiGA::Cli::Action::Env
• #empty_action — MiGA::Cli::Action::Console
• #empty_action — MiGA::Cli::Action::Date
• #empty_action — MiGA::Cli::Action
• #ensure_par — MiGA::Cli
• #ensure_type — MiGA::Cli
• #exclude_newer — MiGA::Cli::Action::Download::Base
• #exit_cleanup — MiGA::Daemon
• #fetch — MiGA::Taxonomy
• #file_path — MiGA::Result
• #finalize_tasks — MiGA::Cli::Action::Download::Base
• #find_software — MiGA::Cli::Action::Init
• #first_preprocessing — MiGA::Dataset::Result
• #flush! — MiGA::Daemon
• #force_task? — MiGA::Dataset::Result::Ignore
• #generic_perform — MiGA::Cli::Action::Download::Base
• #get_job — MiGA::Daemon
• #get_result — MiGA::Common::WithResult
• #highest — MiGA::Taxonomy
• #hook__pull_result_hooks — MiGA::Dataset::Hooks
• #hook__pull_result_hooks — MiGA::Project::Hooks
• #hook_check_type — MiGA::Dataset::Hooks
• #hook_clear_run_counts — MiGA::Dataset::Hooks
• #hook_recalculate_status — MiGA::Dataset::Hooks
• #hook_run_cmd — MiGA::Dataset::Hooks
• #hook_run_cmd — MiGA::Project::Hooks
• #hook_run_lambda — MiGA::Common::Hooks
• #hooks — MiGA::Common::Hooks
• #http_request — MiGA::Common::Net
• #https_request — MiGA::Common::Net
• #ignore_by_type? — MiGA::Dataset::Result::Ignore
• #ignore_complete? — MiGA::Dataset::Result::Ignore
• #ignore_empty? — MiGA::Dataset::Result::Ignore
• #ignore_force? — MiGA::Dataset::Result::Ignore
• #ignore_inactive? — MiGA::Dataset::Result::Ignore
• #ignore_multi? — MiGA::Dataset::Result::Ignore
• #ignore_nomarkers? — MiGA::Dataset::Result::Ignore
• #ignore_nonmulti? — MiGA::Dataset::Result::Ignore
• #ignore_noref? — MiGA::Dataset::Result::Ignore
• #ignore_project? — MiGA::Dataset::Result::Ignore
• #ignore_reasons — MiGA::Dataset::Result::Ignore
• #ignore_task? — MiGA::Project::Result
• #ignore_task? — MiGA::Dataset::Result::Ignore
• #ignore_upstream? — MiGA::Dataset::Result::Ignore
• #import_dataset — MiGA::Project::Dataset
• #import_datasets — MiGA::Cli::Action::Wf
• #impose_limit — MiGA::Cli::Action::Download::Base
• #in? — MiGA::Taxonomy
• #in_loop — MiGA::Common::WithDaemon
• #inactivate! — MiGA::Project::Result
• #inactivate! — MiGA::Dataset
• #info — MiGA::Dataset
• #initialize_empty_project — MiGA::Cli::Action::Wf
• #install_library — MiGA::Cli::Action::Init
• #is_active? — MiGA::Dataset
• #is_clade? — MiGA::Project
• #is_multi? — MiGA::Project
• #is_query? — MiGA::Dataset
• #is_ref? — MiGA::Dataset
• #job_cmd — MiGA::Daemon
• #key — MiGA::Result::Source
• #known_hosts — MiGA::Common::Net
• #l_say — MiGA::Daemon
• #last_alive — MiGA::Common::WithDaemon
• #last_alive — MiGA::Common::WithDaemonClass
• #latency — MiGA::Daemon::Base
• #launch — MiGA::Cli::Action
• #launch — MiGA::Cli
• #launch_daemon — MiGA::Lair
• #launch_daemon_proc — MiGA::Common::WithDaemon
• #launch_job — MiGA::Daemon
• #like_io? — MiGA::MiGA
• #list_requirements — MiGA::Cli::Action::Init
• #load — MiGA::Result
• #load — MiGA::Project
• #load — MiGA::Metadata
• #load_and_filter_datasets — MiGA::Cli::ObjectsHelper
• #load_dataset — MiGA::Cli::ObjectsHelper
• #load_ncbi_taxonomy_dump — MiGA::Cli::Action::Download::Base
• #load_project — MiGA::Cli::ObjectsHelper
• #load_project_or_dataset — MiGA::Cli::ObjectsHelper
• #load_result — MiGA::Cli::ObjectsHelper
• #load_status — MiGA::Daemon
• #load_tasks — MiGA::Cli::Action::Download::Base
• #lock_file — MiGA::Metadata
• #logfh — MiGA::Daemon::Base
• #lowest — MiGA::Taxonomy
• #main_server — MiGA::Common::Net
• #markers? — MiGA::Project
• #markers? — MiGA::Dataset::Type
• #maxjobs — MiGA::Daemon::Base
• #merge_bidir_tmp — MiGA::Cli::Action::Doctor::Distances
• #metadata — MiGA::Dataset
• #miga_name — String
• #miga_name? — String
• #miga_say — MiGA::Daemon
• #miga_variables — String
• #multi? — MiGA::Project
• #multi? — MiGA::Dataset::Type
• #name — MiGA::Cli::Action::Generic
• #name — MiGA::Cli::Action
• #name — MiGA::Project
• #namespace — MiGA::Taxonomy
• #net_method — MiGA::Common::Net
• #next_distances — MiGA::Project::Result
• #next_host — MiGA::Daemon
• #next_inclade — MiGA::Project::Result
• #next_preprocessing — MiGA::Dataset::Result
• #next_task — MiGA::Common::WithResult
• #nodelist — MiGA::Daemon::Base
• #nonmulti? — MiGA::Dataset::Type
• #normalize_encoding — MiGA::Common::Net
• #num_suffix — MiGA::MiGA
• #open_rc_file — MiGA::Cli::Action::Init::FilesHelper
• #opt_common — MiGA::Cli::OptHelper
• #opt_filter_datasets — MiGA::Cli::OptHelper
• #opt_flag — MiGA::Cli::OptHelper
• #opt_object — MiGA::Cli::OptHelper
• #option — MiGA::Common::WithOption
• #option? — MiGA::Common::WithOption
• #option_by_default — MiGA::Common::WithOption
• #option_by_metadata — MiGA::Common::WithOption
• #option_by_metadata — MiGA::Project
• #option_from_string — MiGA::Common::WithOption
• #opts_for_wf — MiGA::Cli::Action::Wf
• #opts_for_wf_distances — MiGA::Cli::Action::Wf
• #outdated_fastaai_ess — MiGA::Cli::Action::Doctor::Base
• #output_file — MiGA::Common::WithDaemon
• #parse — MiGA::Cli
• #parse_cli — MiGA::Cli::Action::SeqcodeGet
• #parse_cli — MiGA::Cli::Action::DerepWf
• #parse_cli — MiGA::Cli::Action::Edit
• #parse_cli — MiGA::Cli::Action::Env
• #parse_cli — MiGA::Cli::Action::Touch
• #parse_cli — MiGA::Cli::Action::Db
• #parse_cli — MiGA::Cli::Action::TaxTest
• #parse_cli — MiGA::Cli::Action::TaxSet
• #parse_cli — MiGA::Cli::Action::Find
• #parse_cli — MiGA::Cli::Action::Date
• #parse_cli — MiGA::Cli::Action::TaxIndex
• #parse_cli — MiGA::Cli::Action::Daemon
• #parse_cli — MiGA::Cli::Action::TaxDist
• #parse_cli — MiGA::Cli::Action::Summary
• #parse_cli — MiGA::Cli::Action::Console
• #parse_cli — MiGA::Cli::Action::Stats
• #parse_cli — MiGA::Cli::Action::Cmd
• #parse_cli — MiGA::Cli::Action::ClassifyWf
• #parse_cli — MiGA::Cli::Action::Archive
• #parse_cli — MiGA::Cli::Action::Doctor
• #parse_cli — MiGA::Cli::Action::Generic
• #parse_cli — MiGA::Cli::Action::Run
• #parse_cli — MiGA::Cli::Action::Get
• #parse_cli — MiGA::Cli::Action::Rm
• #parse_cli — MiGA::Cli::Action::QualityWf
• #parse_cli — MiGA::Cli::Action::GtdbGet
• #parse_cli — MiGA::Cli::Action::AddResult
• #parse_cli — MiGA::Cli::Action::PreprocWf
• #parse_cli — MiGA::Cli::Action::IndexWf
• #parse_cli — MiGA::Cli::Action::Option
• #parse_cli — MiGA::Cli::Action::Ls
• #parse_cli — MiGA::Cli::Action::Add
• #parse_cli — MiGA::Cli::Action::NextStep
• #parse_cli — MiGA::Cli::Action::Lair
• #parse_cli — MiGA::Cli::Action::New
• #parse_cli — MiGA::Cli::Action::About
• #parse_cli — MiGA::Cli::Action
• #parse_cli — MiGA::Cli::Action::Ln
• #parse_cli — MiGA::Cli::Action::NcbiGet
• #parse_cli — MiGA::Cli::Action::Files
• #parse_cli — MiGA::Cli::Action::Init
• #parse_reports_as_datasets — MiGA::Cli::Action::Download::Ncbi
• #partial_bidir_tmp — MiGA::Cli::Action::Doctor::Distances
• #path — MiGA::Result
• #path — MiGA::Daemon
• #perform — MiGA::Cli::Action::Db
• #perform — MiGA::Cli::Action::Ls
• #perform — MiGA::Cli::Action
• #perform — MiGA::Cli::Action::Lair
• #perform — MiGA::Cli::Action::NcbiGet
• #perform — MiGA::Cli::Action::Env
• #perform — MiGA::Cli::Action::New
• #perform — MiGA::Cli::Action::About
• #perform — MiGA::Cli::Action::Init
• #perform — MiGA::Cli::Action::Touch
• #perform — MiGA::Cli::Action::DerepWf
• #perform — MiGA::Cli::Action::Edit
• #perform — MiGA::Cli::Action::NextStep
• #perform — MiGA::Cli::Action::IndexWf
• #perform — MiGA::Cli::Action::TaxTest
• #perform — MiGA::Cli::Action::Option
• #perform — MiGA::Cli::Action::GtdbGet
• #perform — MiGA::Cli::Action::Cmd
• #perform — MiGA::Cli::Action::Ln
• #perform — MiGA::Cli::Action::Files
• #perform — MiGA::Cli::Action::AddResult
• #perform — MiGA::Cli::Action::PreprocWf
• #perform — MiGA::Cli::Action::Get
• #perform — MiGA::Cli::Action::TaxSet
• #perform — MiGA::Cli::Action::QualityWf
• #perform — MiGA::Cli::Action::Date
• #perform — MiGA::Cli::Action::Rm
• #perform — MiGA::Cli::Action::Generic
• #perform — MiGA::Cli::Action::TaxIndex
• #perform — MiGA::Cli::Action::Run
• #perform — MiGA::Cli::Action::Find
• #perform — MiGA::Cli::Action::Doctor
• #perform — MiGA::Cli::Action::SeqcodeGet
• #perform — MiGA::Cli::Action::Archive
• #perform — MiGA::Cli::Action::Daemon
• #perform — MiGA::Cli::Action::ClassifyWf
• #perform — MiGA::Cli::Action::TaxDist
• #perform — MiGA::Cli::Action::Console
• #perform — MiGA::Cli::Action::Summary
• #perform — MiGA::Cli::Action::Stats
• #perform — MiGA::Cli::Action::Add
• #pid_file — MiGA::Common::WithDaemon
• #ppn — MiGA::Daemon::Base
• #print — MiGA::Cli
• #process_alive? — MiGA::Common::WithDaemon
• #profile_advance — MiGA::Dataset::Result
• #profile_datasets_advance — MiGA::Project::Dataset
• #project — MiGA::Result::Source
• #project — MiGA::Project::Result
• #project_daemon — MiGA::Lair
• #project_path — MiGA::Result::Source
• #pull_hook — MiGA::Common::Hooks
• #purge! — MiGA::Daemon
• #puts — MiGA::Cli
• #query? — MiGA::Dataset
• #queue_job — MiGA::Daemon
• #queue_maintenance — MiGA::Daemon
• #read_bidirectional — MiGA::Cli::Action::Doctor::Base
• #read_ncbi_list_json — MiGA::Cli::Action::Download::Ncbi
• #recalculate! — MiGA::Result
• #recalculate? — MiGA::Result
• #recalculate_status — MiGA::Dataset::Status
• #recalculate_tasks — MiGA::Common::WithResult
• #ref? — MiGA::Dataset
• #relative_dir — MiGA::Result::Source
• #relative_path — MiGA::Result::Source
• #reload_project — MiGA::Daemon
• #remote_connection — MiGA::Common::Net
• #remote_list — MiGA::Cli::Action::Download::Ncbi
• #remote_list — MiGA::Cli::Action::Download::Gtdb
• #remote_list — MiGA::Cli::Action::Download::Seqcode
• #remote_list_query — MiGA::Cli::Action::Download::Ncbi
• #remote_report_name — MiGA::Cli::Action::Download::Ncbi
• #remote_row_name — MiGA::Cli::Action::Download::Gtdb
• #remote_row_name — MiGA::Cli::Action::Download::Seqcode
• #remove! — MiGA::Result
• #remove! — MiGA::Metadata
• #remove! — MiGA::Dataset
• #reset — MiGA::Taxonomy
• #reset_action — MiGA::Cli
• #result — MiGA::Common::WithResult
• #result_base — MiGA::Project::Result
• #result_base — MiGA::Dataset::Result
• #result_dirs — MiGA::Common::WithResult
• #result_files_exist? — MiGA::MiGA
• #result_status — MiGA::Dataset::Result
• #results — MiGA::Common::WithResult
• #results_status — MiGA::Dataset::Result
• #root_path — MiGA::Common::Path
• #run — MiGA::Common::WithDaemon
• #run — MiGA::SQLite
• #run_block — MiGA::SQLite
• #run_cmd — MiGA::Cli::Action::Doctor::Base
• #run_cmd — MiGA::Common::SystemCall
• #run_cmd — MiGA::Cli::Action::Init
• #run_cmd_opts — MiGA::Common::SystemCall
• #run_daemon — MiGA::Cli::Action::Wf
• #run_r_cmd — MiGA::Cli::Action::Init
• #running_time — MiGA::Result::Dates
• #runopts — MiGA::Daemon::Base
• #runopts_for — MiGA::Daemon::Base
• #sanitize_cli — MiGA::Cli::Action::Download::Gtdb
• #sanitize_cli — MiGA::Cli::Action::Download::Seqcode
• #sanitize_cli — MiGA::Cli::Action::Download::Ncbi
• #save — MiGA::Result
• #save — MiGA::Metadata
• #save — MiGA::Project
• #save — MiGA::Dataset
• #save! — MiGA::Project
• #save! — MiGA::Dataset
• #save! — MiGA::Metadata
• #save_bidirectional — MiGA::Cli::Action::Doctor::Base
• #save_entry — MiGA::Cli::Action::Download::Base
• #save_status — MiGA::Daemon
• #saved_targets — MiGA::Cli::Action::Doctor::Base
• #say — MiGA::MiGA
• #say — MiGA::Daemon
• #say — MiGA::Cli
• #script_path — MiGA::Common::Path
• #seqs_length — MiGA::Common::Format
• #set_option — MiGA::Common::WithOption
• #show_log! — MiGA::Daemon::Base
• #show_log? — MiGA::Daemon::Base
• #show_summary! — MiGA::Daemon::Base
• #shutdown_when_done? — MiGA::Daemon::Base
• #skip_maintenance — MiGA::Daemon::Base
• #sorted_ranks — MiGA::Taxonomy
• #source — MiGA::Result::Source
• #start — MiGA::Common::WithDaemon
• #started_at — MiGA::Result::Dates
• #stats — MiGA::Result::Stats
• #status — MiGA::Dataset::Status
• #status — MiGA::Common::WithDaemon
• #stop — MiGA::Common::WithDaemon
• #summarize — MiGA::Cli::Action::Wf
• #table — MiGA::Cli
• #tabulate — MiGA::Common::Format
• #task_description — MiGA::Cli
• #tax_str — MiGA::TaxIndexTaxon
• #taxa_by_rank — MiGA::TaxIndex
• #terminate — MiGA::Common::WithDaemon
• #terminate_daemon — MiGA::Lair
• #terminate_daemons — MiGA::Lair
• #terminate_file — MiGA::Common::WithDaemon
• #terminated_file — MiGA::Common::WithDaemonClass
• #terminated_file — MiGA::Common::WithDaemon
• #termination_file? — MiGA::Common::WithDaemon
• #test_library — MiGA::Cli::Action::Init
• #to_h — MiGA::Cli
• #to_hash — MiGA::TaxIndexTaxon
• #to_json — MiGA::Metadata
• #to_json — MiGA::TaxIndex
• #to_json — MiGA::TaxIndexTaxon
• #to_json — MiGA::Taxonomy
• #to_s — MiGA::Taxonomy
• #to_tab — MiGA::TaxIndexTaxon
• #to_tab — MiGA::TaxIndex
• #transfer_metadata — MiGA::Cli::Action::Wf
• #type — MiGA::Project
• #type — MiGA::Dataset::Type
• #unlink — MiGA::Result
• #unlink_dataset — MiGA::Project::Dataset
• #unlink_entries — MiGA::Cli::Action::Download::Base
• #unmiga_name — String
• #unregistered_datasets — MiGA::Project::Dataset
• #update_format_0 — MiGA::Daemon
• #updated — MiGA::Metadata
• #verbosity — MiGA::Daemon::Base
• #versions — MiGA::Result::Versions
• #versions_md — MiGA::Result::Versions
• #why_ignore — MiGA::Dataset::Result::Ignore
• #wrap_width — String
• #write_alive_file — MiGA::Common::WithDaemon
• #write_ncbi_list_json — MiGA::Cli::Action::Download::Ncbi